[2024-01-24 10:57:50,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,265] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,265] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf735416-e1b6-4e29-a9c2-bdee8e625674/dqc_reference
[2024-01-24 10:57:52,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,641] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,642] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdd6deee-41e2-4924-ac33-055db63f8f4c/GCF_007830035.1_ASM783003v1_genomic.fna.gz | prodigal -d GCF_007830035.1_ASM783003v1_genomic.fna/cds.fna -a GCF_007830035.1_ASM783003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:03,726] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:03,726] [INFO] Task started: HMMsearch
[2024-01-24 10:58:03,727] [INFO] Running command: hmmsearch --tblout GCF_007830035.1_ASM783003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf735416-e1b6-4e29-a9c2-bdee8e625674/dqc_reference/reference_markers.hmm GCF_007830035.1_ASM783003v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:03,996] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:03,997] [INFO] Found 6/6 markers.
[2024-01-24 10:58:04,028] [INFO] Query marker FASTA was written to GCF_007830035.1_ASM783003v1_genomic.fna/markers.fasta
[2024-01-24 10:58:04,028] [INFO] Task started: Blastn
[2024-01-24 10:58:04,028] [INFO] Running command: blastn -query GCF_007830035.1_ASM783003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf735416-e1b6-4e29-a9c2-bdee8e625674/dqc_reference/reference_markers.fasta -out GCF_007830035.1_ASM783003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:04,911] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:04,920] [INFO] Selected 20 target genomes.
[2024-01-24 10:58:04,921] [INFO] Target genome list was writen to GCF_007830035.1_ASM783003v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:04,947] [INFO] Task started: fastANI
[2024-01-24 10:58:04,947] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdd6deee-41e2-4924-ac33-055db63f8f4c/GCF_007830035.1_ASM783003v1_genomic.fna.gz --refList GCF_007830035.1_ASM783003v1_genomic.fna/target_genomes.txt --output GCF_007830035.1_ASM783003v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:20,718] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:20,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf735416-e1b6-4e29-a9c2-bdee8e625674/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:20,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf735416-e1b6-4e29-a9c2-bdee8e625674/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:20,740] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:20,740] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:20,740] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	100.0	1168	1169	95	conclusive
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	83.3886	804	1169	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	82.1353	677	1169	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	81.796	669	1169	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	81.7702	609	1169	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	81.5195	606	1169	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	81.3728	530	1169	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.2503	527	1169	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.2265	604	1169	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	81.1342	563	1169	95	below_threshold
Luteimonas panaciterrae	strain=Gsoil 068	GCA_020511115.1	363885	363885	type	True	81.1235	631	1169	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	80.9952	659	1169	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	80.9193	664	1169	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	80.8226	568	1169	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	80.7435	589	1169	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014396975.1	1463158	1463158	type	True	80.5238	583	1169	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	80.4431	644	1169	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	80.4218	649	1169	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	80.1574	600	1169	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	80.0182	542	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:20,742] [INFO] DFAST Taxonomy check result was written to GCF_007830035.1_ASM783003v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:20,742] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:20,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:20,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf735416-e1b6-4e29-a9c2-bdee8e625674/dqc_reference/checkm_data
[2024-01-24 10:58:20,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:20,779] [INFO] Task started: CheckM
[2024-01-24 10:58:20,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830035.1_ASM783003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830035.1_ASM783003v1_genomic.fna/checkm_input GCF_007830035.1_ASM783003v1_genomic.fna/checkm_result
[2024-01-24 10:58:58,704] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:58,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:58,727] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:58,727] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:58,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830035.1_ASM783003v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:58,728] [INFO] Task started: Blastn
[2024-01-24 10:58:58,728] [INFO] Running command: blastn -query GCF_007830035.1_ASM783003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf735416-e1b6-4e29-a9c2-bdee8e625674/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830035.1_ASM783003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:00,290] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:00,296] [INFO] Selected 22 target genomes.
[2024-01-24 10:59:00,296] [INFO] Target genome list was writen to GCF_007830035.1_ASM783003v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:00,322] [INFO] Task started: fastANI
[2024-01-24 10:59:00,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdd6deee-41e2-4924-ac33-055db63f8f4c/GCF_007830035.1_ASM783003v1_genomic.fna.gz --refList GCF_007830035.1_ASM783003v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830035.1_ASM783003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:21,091] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:21,117] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:21,117] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_007830035.1	s__Luteimonas_C cucumeris	100.0	1168	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902825775.1	s__Luteimonas_C sp902825775	83.6919	814	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239095.1	s__Luteimonas_C gilva	83.3809	804	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422305.1	s__Luteimonas mephitis	82.0675	665	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	81.8455	665	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337105.1	s__Thermomonas sp006337105	81.5657	601	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	81.3679	727	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_001428685.1	s__Lysobacter sp001428685	81.3402	720	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.42	98.61	0.98	0.96	4	-
GCA_014380115.1	s__JACMKK01 sp014380115	81.3115	501	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JACMKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320095.1	s__Luteimonas_B telluris	81.2838	510	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768335.1	s__Lysobacter arseniciresistens	81.1101	565	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829315.1	s__Xanthomonas_A translucens_A	81.0976	679	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	80.9296	663	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362405.1	s__JABFWF01 sp013362405	80.9275	461	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018406645.1	s__Lysobacter_A helvus	80.8942	555	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014206815.1	s__Xanthomonas_A sacchari_B	80.8696	652	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010093345.1	s__Pseudoxanthomonas_A yeongjuensis	80.7833	645	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	80.7276	474	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526085.1	s__SCMT01 sp011526085	80.5765	603	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004284655.1	s__Pseudoxanthomonas_A spadix_A	80.2688	597	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	98.46	98.41	0.91	0.91	3	-
GCA_002240395.1	s__Luteimonas citri_A	80.2192	553	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284595.1	s__Stenotrophomonas maltophilia_F	79.984	563	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.76	98.38	0.92	0.88	60	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:21,119] [INFO] GTDB search result was written to GCF_007830035.1_ASM783003v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:21,120] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:21,125] [INFO] DFAST_QC result json was written to GCF_007830035.1_ASM783003v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:21,125] [INFO] DFAST_QC completed!
[2024-01-24 10:59:21,125] [INFO] Total running time: 0h1m31s